On Fri, Jan 26, 2024, Yu Chen via AMBER wrote:
>
>
>The residue numbering for GPCR adheres to the Ballesteros Weinstein
>numbering system. Therefore, it is crucial for the output system PDB file
>to maintain this numbering. However, I’ve noticed that after inputting
>the original protein PDB (where the residue number starts from, for
>instance, 66) into AmberTools, the residue numbering in the output system
>PDB file starts from 1. This discrepancy poses a challenge when identifying
>key interactions with certain reserved GPCR residues during post-MD
>analysis.
This is possible; it is a little complex, but really not very hard.
After you build the system, fire up ParmEd, and use the addPdb action to get
the original residue numbers and chain ID's into the prmtop file.
Once the simulation is done, you can use the "-ext" flag to ambpdb to create
a PDB file that has the original residue numbers, etc. in it. That might be
enough for many purposes.
Cpptraj also knows how to perform analyses using the original residue
numbers. Look at Section 36.3.2 (for the "::" and ":;" elements in the mask
syntax). Let us know if you need help.
...good luck...dac
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Received on Fri Jan 26 2024 - 15:00:02 PST
